Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of <i>Cordyceps sinensis</i> (Chinese <i>Cordyceps</i>), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese <i>Cordyceps</i> has caused vegetation degradation and impacted the sustainable occurrence of <i>Cordyceps</i>. The effects of Chinese <i>Cordyceps</i> collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. <i>C</i>. <i>sinensis</i> collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In <i>Cordyceps</i> production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese <i>Cordyceps</i> enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese <i>Cordyceps</i> production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the <i>Cordyceps</i> production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.